Sum of Regressors and Regressors of Interest Missing

[skrivonosov]

Hello everyone!

I have been using a set of scripts to preprocess fMRI data for a study involving irritability tasks. These scripts have worked without issues for a long time. However, after updating to AFNI version AFNI_24.3.05 ('Elagabalus'), I've encountered a problem. While the preprocessing completes successfully and the QC files are generated, the "sum of regressors" and "regressors of interest" plots are missing from the output.

No changes have been made to the scripts themselves. Has anyone else encountered this problem or have suggestions on how to resolve it?

Thank you in advance for your help!

[ptaylor]

Howdy-

Could you please copy+paste the output of:

afni_system_check.py -check_all

?

--pt

[skrivonosov]

Yes, here it is!

Sorry in advance it's a little small.

[ptaylor]

Hi-

Sorry, I can't read that. Could you please copy+paste the text, as text?

There is some built-in functionality to this Message Board that helps make copy+pasted code more easily readable, for both large code chunks and "within line" text.

A couple different ways of doing so are described here. In particular, you can simply wrap large segments of code between "triple backticks".

This will make it easier for us and others to read and interact with your code.

thanks,
pt

[rickr]

It looks like the error relates to using matplotlib with numpy 2.2.2.

[skrivonosov]

I was able to fix the matplotlib with numpy 2.2.2 issue, and some of the missing sections load now. However, there are still some missing sections, some that weren't previously missing that are now. Here is the updated output from the afni_system_check.py -check_all command:

-------------------------------- general ---------------------------------
architecture:         64bit ELF
cpu type:             x86_64
system:               Linux
release:              6.8.0-52-generic
version:              #53~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Wed Jan 15 19:18:46 UTC 2
distribution:         ubuntu 22.04 Jammy Jellyfish
number of CPUs:       40
apparent login shell: tcsh
shell RC file:        .tcshrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni           : /usr/local/afni/afni
afni version         : Precompiled binary linux_ubuntu_16_64: Oct 26 2024 
                     : AFNI_24.3.05 'Elagabalus'
AFNI_version.txt     : AFNI_24.3.05, linux_ubuntu_16_64, Oct 26 2024, official
which python         : /usr/bin/python
python version       : 3.10.12
which R              : /usr/bin/R
R version            : R version 4.4.3 (x86_64-pc-linux-gnu)

instances of various programs found in PATH:
    afni    : 1   (/usr/local/afni/afni)
    R       : 1   (/usr/bin/R)
    python  : 1   (/usr/bin/python3.10)
    python2 : 0 
    python3 : 1   (/usr/bin/python3.10)

testing ability to start various programs...
    afni                 : success
    suma                 : success
    3dSkullStrip         : success
    3dAllineate          : success
    3dRSFC               : success
    SurfMesh             : success
    3dClustSim           : success
    uber_subject.py      : success
    3dMVM                : success

------------------------ dependent program tests -------------------------
checking for dependent programs...

which tcsh           : /usr/bin/tcsh
tcsh version         : 6.21.00
which Xvfb           : /usr/bin/Xvfb

checking for R packages...
    rPkgsInstall -pkgs ALL -check : success

R RHOME : /usr/lib/R

------------------------------ python libs -------------------------------
++ module loaded: matplotlib.pyplot
   module file : /usr/lib/python3/dist-packages/matplotlib/pyplot.py
   matplotlib version : 3.5.1

++ module loaded: flask
   module file : /usr/lib/python3/dist-packages/flask/__init__.py
   flask version : 2.0.1

++ module loaded: flask_cors
   module file : /usr/lib/python3/dist-packages/flask_cors/__init__.py
   flask_cors version : 3.0.9

-------------------------------- env vars --------------------------------
PATH                       = /usr/local/afni:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni

PYTHONPATH                 = 
R_LIBS                     = /usr/local/R_libs
LD_LIBRARY_PATH            = 
DYLD_LIBRARY_PATH          = 
DYLD_FALLBACK_LIBRARY_PATH = 
CONDA_SHLVL                = 
CONDA_DEFAULT_ENV          = 
CC                         = 

----------------------------- eval dot files -----------------------------

----------- AFNI $HOME files -----------

    .afnirc                   : found
    .sumarc                   : found
    .afni/help/all_progs.COMP : found
--------- shell startup files ----------

   -- good: .tcshrc seems to contain 'source .cshrc'
   -- considered operations: path, apsearch
   
   -- note: followers should not need edits, so edit flags should be 0
      (have 1 follower(s), which can be ignored)
   
   dot file test : want 1 modifications across 2 files:
   
      file             path  flatdir  apsearch        follower
      ---------------  ----  -------  --------        --------
      .cshrc           0     0        1               0     
      .tcshrc          0     0        0               1     
   
------------------------------ data checks -------------------------------
data dir : missing AFNI_data6
data dir : missing AFNI_demos
data dir : missing suma_demo
data dir : missing afni_handouts
atlas    : found TT_N27+tlrc  under /usr/local/afni

------------------------------ OS specific -------------------------------
which apt-get        : /usr/bin/apt-get
apt-get version      : apt 2.4.13 (amd64)

have Ubuntu system: ubuntu 22.04 Jammy Jellyfish
have Ubuntu afni  : Precompiled binary linux_ubuntu_16_64: Oct 26 2024 

=========================  summary, please fix:  =========================
*  dot file test : want 1 modifications across 2 files:
*  insufficient data for AFNI bootcamp
   (see "Prepare for Bootcamp" on install pages)

[ptaylor]

OK, glad to hear that the numpy issue is resolved.

What section(s) are missing at present? That system check output (thanks for sending that) looks reasonable to me.

Also, could you please copy+paste the afni_proc.py command that you are running?

--pt

[skrivonosov]

The section missing is the grayplot, which is present in the output file just no graph is actually appearing.

This is the afni_proc.py command:

afni_proc.py -subj_id $subjID   \
        -tcat_remove_first_trs 9 \
        -script proc.${subjID}_FDp3 -scr_overwrite   \
        -blocks tshift align tlrc volreg blur mask scale regress   \
        -copy_anat $anat   \
        -dsets   \
                scan*Frustration*+orig.HEAD   \
        -volreg_align_to last   \
        -volreg_align_e2a   \
        -align_opts_aea -cost lpc+zz -giant_move -AddEdge   \
           -epi_strip 3dSkullStrip   \
        -tlrc_NL_warp   \
        -volreg_tlrc_warp   \
        -regress_stim_times   \
            stim_times/subj*_stim0_Cue_After_RiggedHit.txt   \
            stim_times/subj*_stim1_Cue_After_NonRiggedHit.txt   \
            stim_times/subj*_stim2_Cue_After_NonRiggedMiss.txt   \
            stim_times/subj*_stim3_Target-Hit.txt   \
            stim_times/subj*_stim4_Target-Miss.txt   \
            stim_times/subj*_stim5_Feedback-Rigged-Hit.txt   \
            stim_times/subj*_stim6_Feedback-Nonrigged-Hit.txt   \
            stim_times/subj*_stim7_Feedback-Nonrigged-Miss.txt   \
        -regress_stim_labels   \
            $prefix.AfterRiggedHit_Cue $prefix.AfterNonRiggedHit_Cue $prefix.AfterNonRiggedMiss_Cue \
            $prefix.TargetHit $prefix.TargetMiss   \
            $prefix.RiggedHit $prefix.NonriggedHit $prefix.NonriggedMiss   \
        -regress_basis_multi   \
            'dmBLOCK' 'dmBLOCK' 'dmBLOCK' \
            'BLOCK(1.5,1)' 'BLOCK(1.5,1)' \
            'BLOCK(3,1)' 'BLOCK(3,1)' 'BLOCK(3,1)'\
        -regress_stim_types AM1 AM1 AM1 times times times times times \
        -regress_censor_motion $motion_max   \
        -regress_compute_fitts   \
        -regress_opts_3dD   \
            -jobs 8   \
            -regress_local_times   \
        -regress_make_ideal_sum sum_ideal.1D   \
        -regress_est_blur_epits   \
        -regress_est_blur_errts   \
        -regress_make_cbucket yes

[ptaylor]

Hm, OK. And are there other JPG images, like the lines plots under motion that might look kind of like this:

? In some systems that have had this issue, the libjpeg library was missing, which is what this might inform about.

What happens if you run this in your AP results directory:

    3dGrayplot                                                               \
        -polort   -1                                                         \
        -pvorder                                                             \
        -dimen    1800 500                                                   \
        -range    3.29                                               \
        -input    errts*HEAD                                             \
        -mask     mask_epi_anat*.HEAD                                         \
        -prefix   TEST_GRAYPLOT

?

thanks,
pt